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Introduction to Linux - A Hands on Guide

This guide was created as an overview of the Linux Operating System, geared toward new users as an exploration tour and getting started guide, with exercises at the end of each chapter.
For more advanced trainees it can be a desktop reference, and a collection of the base knowledge needed to proceed with system and network administration. This book contains many real life examples derived from the author's experience as a Linux system and network administrator, trainer and consultant. They hope these examples will help you to get a better understanding of the Linux system and that you feel encouraged to try out things on your own.

I'm having load times issues with a few sites I'm hosting on a dedicated server. I'll try to be as detailed as I can.

I'm hosting a few sites (phpbb forum and some other simple sites) on a Centos 6.4, with 8GB of ram and a Quad Core processor. Two hard disks in software raid1.
A few days ago I had to move the machine from one DC to another (the new one is better and since then the issues occurred.
Currently I'm having slow loading times on almost all sites, mainly on the phpbb forum (forum is quite big - ~10.000 registered, 250.000 posts).
My php version is 5.4.16, mysql is 5.5.32 and apache is 2.4.0.
I've been researching almost everything on the machine and I found a few... lets say symptoms that might be causing this issue, but I don't know how to proceed in investigating them.

I started monitoring memory usage, but there are no issues there.
I started recieving the following reports:

CPU usage for one of the cores starts going up to 100% for 1 or 2 seconds and than drops down again. Most of the times it's a HTTPD process.
I also monitored iotop and this caught my attention, although i have no idea what it means:

I also noticed something strange, that didn't happen before. I don't know if it is relevant or not. Sometimes the SSH session just hang for a few (1-4 seconds). I mean while writing, moving up and down pages, etc...

So I've been banging my head with this issue for the last 4-5 days and I'm at a dead end. No idea what to do or what is causing this, since no other changes were made except the migration.

Edit: Ok. So I could officially rule out an issue with the mysql database. I moved the most loaded DB on another server, loading times for the DB went from 7s to 0.36s, but the site (forum in my case) still loads extremely slow.